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Biophys J. 2011 Aug 17;101(4):951-60. doi: 10.1016/j.bpj.2011.06.043.

Multiple replica repulsion technique for efficient conformational sampling of biological systems.

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  • 1Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada. anatoly.malevanets@gmail.com

Abstract

Here, we propose a technique for sampling complex molecular systems with many degrees of freedom. The technique, termed "multiple replica repulsion" (MRR), does not suffer from poor scaling with the number of degrees of freedom associated with common replica exchange procedures and does not require sampling at high temperatures. The algorithm involves creation of multiple copies (replicas) of the system, which interact with one another through a repulsive potential that can be applied to the system as a whole or to portions of it. The proposed scheme prevents oversampling of the most populated states and provides accurate descriptions of conformational perturbations typically associated with sampling ground-state energy wells. The performance of MRR is illustrated for three systems of increasing complexity. A two-dimensional toy potential surface is used to probe the sampling efficiency as a function of key parameters of the procedure. MRR simulations of the Met-enkephalin pentapeptide, and the 76-residue protein ubiquitin, performed in presence of explicit water molecules and totaling 32 ns each, investigate the ability of MRR to characterize the conformational landscape of the peptide, and the protein native basin, respectively. Results obtained for the enkephalin peptide reflect more closely the extensive conformational flexibility of this peptide than previously reported simulations. Those obtained for ubiquitin show that conformational ensembles sampled by MRR largely encompass structural fluctuations relevant to biological recognition, which occur on the microsecond timescale, or are observed in crystal structures of ubiquitin complexes with other proteins. MRR thus emerges as a very promising simple and versatile technique for modeling the structural plasticity of complex biological systems.

Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

PMID:
21843487
[PubMed - indexed for MEDLINE]
PMCID:
PMC3175088
Free PMC Article
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